Not sure what I did wrong to have a submenu, Setting->Technical->Custom Shortcuts, under which there are a number of all the same shortcut modules 'Quotations' and it is annoying in terms of interface as there is already a web shortcuts on top-right, just next to user icon.

You are talking about menu shortcut which are listed in below user icon in side corner of web interface.
Suppose "Quotation" menu shortcut is added in that list.
for remove this link just open "quotation" menu and In right-corner of Form. you may find this [] icon in yellow color it means it pressed already so just press [] this icon and un highlight it.

Now you can see this custom shortcut list in below user icon. It will removed

For find more information about how works menu shortcut jump to this link